11-35489359-T-G

Position:

• chr11-35489359-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001001991.3(PAMR1):​c.379+2686A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.544 in 152,056 control chromosomes in the GnomAD database, including 26,299 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.54 (26299 hom., cov: 31)
• Consequence: PAMR1 NM_001001991.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.410

Genes affected

PAMR1 (HGNC:24554): (peptidase domain containing associated with muscle regeneration 1) Predicted to enable calcium ion binding activity and serine-type endopeptidase activity. Predicted to be involved in proteolysis. Predicted to be located in extracellular region. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.697 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PAMR1	NM_001001991.3	c.379+2686A>C		intron_variant		ENST00000619888.5	NP_001001991.1
PAMR1	NM_015430.4	c.379+2686A>C		intron_variant			NP_056245.2
PAMR1	NM_001282675.2	c.259+2686A>C		intron_variant			NP_001269604.1
PAMR1	NM_001282676.2	c.379+2686A>C		intron_variant			NP_001269605.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PAMR1	ENST00000619888.5	c.379+2686A>C		intron_variant		1	NM_001001991.3	ENSP00000483703.1

Frequencies

GnomAD3 genomes AF: 0.544 AC: 82636 AN: 151938 Hom.: 26293 Cov.: 31

Gnomad AFR AF: 0.199

Gnomad AMI AF: 0.726

Gnomad AMR AF: 0.613

Gnomad ASJ AF: 0.705

Gnomad EAS AF: 0.420

Gnomad SAS AF: 0.552

Gnomad FIN AF: 0.760

Gnomad MID AF: 0.563

Gnomad NFE AF: 0.702

Gnomad OTH AF: 0.571

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.544 AC: 82645 AN: 152056 Hom.: 26299 Cov.: 31 AF XY: 0.545 AC XY: 40481 AN XY: 74314

Gnomad4 AFR AF: 0.198

Gnomad4 AMR AF: 0.613

Gnomad4 ASJ AF: 0.705

Gnomad4 EAS AF: 0.420

Gnomad4 SAS AF: 0.552

Gnomad4 FIN AF: 0.760

Gnomad4 NFE AF: 0.702

Gnomad4 OTH AF: 0.573

Alfa AF: 0.669 Hom.: 47320

Bravo AF: 0.520

Asia WGS AF: 0.452 AC: 1572 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.6
DANN	Benign	0.60

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs10768140; hg19: chr11-35510907;